Hello,
I am new to FSL. I was wondering if anybody here could answer some questions in regard to "Intro Practical".
1. In the last sentence of "Viewing Atlases", ".. with the full probability information shown as a gradation of colour." What is the convention used in the gradation of color?
2. Under "Viewing the results" in BET. "Change the transparency and colour of the overlay so that you can get a better view of the successes of the brain extraction." How do I change the colour?
3. Under "fslstats" in FSLUTILS, "Slightly confusingly, the robust range doesn't seem to be doing the same thing for the left and right tails." What do you mean here?
4. "Click on the histogram toolbox button [3] and turn off the ignore zeros and press OK." After I turned off "ignore zeros", I saw a spike of amplitude about 6.9e6 at zero. Is this because of "lots of empty voxels in the image (because the data has been brain-extracted)"?
5. "Now it is clear that the robust range limits make more sense." I don't understand.
a. When I issued "fslstats highres -R -r", I got: 0.0 32767 0 16711.1699. In the histogram, there is a hill-like shape from 0 to 2.1e4. Then, the signal approaches zero with a small peak (a triangle) at around 3.3e4. So, an absolute range of [0 32767] makes sense. As for the robust range, it is [0 16711.1699]. From the histogram, 1.6e4 is not the tail. About 2.2e4 is. Could you please let me know why it gave 1.6e4 rather than a value around 2.2e4?
b.When I unchecked "ignore zero", I saw a large spike of amplitude about 6.85e6 at 0 intensity. Is this because the data has been extracted so that there are lots of empty voxels in the image?
c. When I issued "fslstats highres -1 1 -R -r", I got: 11.0 32767.0 2696.99 18976.72. The histogram shows that there are non-zero number of voxels from Intensity 0 to about 2.3e4. Why a robust range of [2696.99 18976.72] makes more sense?
d. When I issued "fslview egepi" and viewed the histogram, I found the curve approaching the x and y axes asymptotically. The number of voxels with zero intensity is 36345. In the case of highres, the number of voxels with zero intensity is 7e6. So, there are fewer voxels with exactly 0 intensity as the text mentioned. Why?
e. In egepi, the tail of the histogram can be considered from Intensity 3000 to 2e4. The tail of highres is from around 2e4 to 3.5e4 which is longer. By "large tail of very low background voxels", do you just look at the curve of egepi alone rather than comparing it with the curve in highres? Why highres has a longer tail and at a higher Intensity than the egepi curve?
Thanks.
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